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Cited by 77Chemical and Physical StudiesProtein Structure and DynamicsRNA and protein synthesis mechanisms

From Water and Ions to Crowded Biomacromolecules: In Vivo Structuring of a Prokaryotic Cell

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Spitzer, Jan·2011·Microbiology and Molecular Biology Reviews
DOI 10.1128/mmbr.00010-11PMC PMC3165543
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Abstract

The interactions and processes which structure prokaryotic cytoplasm (water, ions, metabolites, and biomacromolecules) and ensure the fidelity of the cell cycle are reviewed from a physicochemical perspective. Recent spectroscopic and biological evidence shows that water has no active structuring role in the cytoplasm, an unnecessary notion still entertained in the literature; water acts only as a normal solvent and biochemical reactant. Subcellular structuring arises from localizations and interactions of biomacromolecules and from the growth and modifications of their surfaces by catalytic reactions. Biomacromolecular crowding is a fundamental physicochemical characteristic of cells in vivo. Though some biochemical and physiological effects of crowding (excluded volume effect) have been documented, crowding assays with polyglycols, dextrans, etc., do not properly mimic the compositional variety of biomacromolecules in vivo. In vitro crowding assays are now being designed with proteins, which better reflect biomacromolecular environments in vivo, allowing for hydrophobic bonding and screened electrostatic interactions. I elaborate further the concept of complex vectorial biochemistry, where crowded biomacromolecules structure the cytosol into electrolyte pathways and nanopools that electrochemically "wire" the cell. Noncovalent attractions between biomacromolecules transiently supercrowd biomacromolecules into vectorial, semiconducting multiplexes with a high (35 to 95%)-volume fraction of biomacromolecules; consequently, reservoirs of less crowded cytosol appear in order to maintain the experimental average crowding of ∼25% volume fraction. This nonuniform crowding model allows for fast diffusion of biomacromolecules in the uncrowded cytosolic reservoirs, while the supercrowded vectorial multiplexes conserve the remarkable repeatability of the cell cycle by preventing confusing cross talk of concurrent biochemical reactions.

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  • Young Earth conditions may have facilitated the production of nitrogen-reduced compounds, such as HCN and cyanoacetylene.

    “These conditions may have facilitated the production of nitrogen-reduced compounds, such as HCN and cyanoacetylene.”

    From The Origin and Early Evolution of Life: Homochirality Emergence in Prebiotic Environments (2023) · cites this paper as Spitzer, 2011

    The Introduction says life most likely arose in hot, salty water, but does not connect early-Earth conditions to the production of nitrogen-reduced compounds. Searches for HCN, cyanoacetylene, and reduced nitrogen found no passage addressing that production claim in our copy. (LLM, conf=0.72)

    Experimental — accuracy not yet measured

  • HCN and cyanoacetylene could have accumulated and concentrated in lakes or enclosed pools.

    “Such products could have accumulated and concentrated in lakes or enclosed pools.”

    From The Origin and Early Evolution of Life: Homochirality Emergence in Prebiotic Environments (2023) · cites this paper as Spitzer, 2011

    The Introduction discusses water, early life, and crowded cell interiors, but the passages found do not address whether HCN or cyanoacetylene could accumulate in lakes or enclosed pools. Searches for those compounds and for prebiotic concentration in lakes or ponds found no supporting passage in our copy. (LLM, conf=0.72)

    Experimental — accuracy not yet measured

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Cited by

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Authors
Spitzer, J.
Affiliations
Mallard Creek Polymers, Inc., 14700 Mallard Creek Road, Charlotte, North Carolina 28262
Corresponding author
Spitzer, Jan
ORCID
Spitzer, Jan
Venue
Microbiology and Molecular Biology Reviews
Publisher
American Society for Microbiology
Published
2011-09
Volume
75
Issue
3
Pages
491-506
ISSN
  • 1092-2172 (ISSN-L)
  • 1098-5557
DOI
10.1128/mmbr.00010-11
PMC
PMC3165543
OpenAlex
W2162013578
Cited by
77
References
9
Citations by year
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FWCI
0.81
Type
journal article
Language
en
Open access
Licence
journals.asm.org/non-commercial-tdm-license (tdm)
Locations
  • Microbiology and Molecular Biology Reviews (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Chemical and Physical Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
excluded volume, non-covalent interactions, hydrophobic interactions
MeSH terms
Ions, Models, Biological, Prokaryotic Cells, Water, Intracellular Space, Macromolecular Substances

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